In early 2367, the Saratoga was part of the fleet of forty starships massed at Wolf 359 in defense of Sector 001 during an incursion by a Borg cube. During the battle, the cube locked the Saratoga in a tractor beam, draining her shields until they eventually failed. The Borg then fired a cutting beam at the Saratoga, scoring a direct hit on decks 1 through 4, as well as causing devastating damage. Most notably, the warp core suffered heavy damage that would lead to antimatter containment failure. Many died, including the captain. The first officer, Lieutenant Commander Benjamin Sisko, ordered the crew and civilians to escape pods. Commander Sisko escaped with his son Jake, but his wife Jennifer perished during the attack. The ship was ultimately destroyed by a Borg cutting beam in combination with a warp core breach. (DS9: "Emissary")
The Saratoga was a reuse of the USS Reliant studio model built for Star Trek II: The Wrath of Khan, relabeled with a new registry. This time around, however, the model was filmed without a "roll bar" like the USS Lantree and two large outboard modules (ostensibly referred to by production sources as sensor pods) were installed. The ship fired phasers from an area usually identified as the lower sensor dome, rather than from any of the phaser emplacements built into the model. It was also mentioned in "Emissary" that the Saratoga was equipped with photon torpedoes, but the ship was never seen firing any at all, and the location of the torpedo launchers was never made clear.
The Saratoga destruction sequence, along with the other Wolf 359 visual effects sequences, was one of the first scenes filmed for "Emissary", during pre-production on the pilot episode. The sequence was shot on a Paramount sound stage, rather than at Image G due to safety reasons over the use of explosives. Three takes were required to achieve the desired detonation – using all three breakaway models built for the sequence. (Movie Magic – "Space Effects: The Space Race")
The ship's dedication plaque is visible, albeit briefly, on the bridge during the battle scene in "Emissary", though the text is not legible.
In the Star Trek Online mission "State of Q" (prior to its being removed), the Iconians send a number of Borg drones back in time to the Saratoga during the Battle of Wolf 359, with the intention of killing Benjamin Sisko and changing history. Q sends the player back to stop them. The Borg also invade the Saratoga in the game Star Trek: Deep Space Nine - Crossroads of Time. The novel Saratoga features survivors of the vessel.